[English] 日本語
Yorodumi
- PDB-8cmo: Cryo-EM structure of the Photosystem I - LHCI supercomplex from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cmo
TitleCryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.
Components
  • (Light-harvesting protein of photosystem I ...) x 9
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 6
  • (Photosystem I subunit ...) x 2
  • Photosystem I reaction centre subunit XI PsaL
KeywordsPHOTOSYNTHESIS / Green alga / PSI / Coelastrella / membrane protein / Cryo-EM
Function / homology
Function and homology information


1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / LAURIC ACID / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / LAURIC ACID / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LPX / Chem-LUT / Chem-NKP / OCTANOIC ACID (CAPRYLIC ACID) / PHYLLOQUINONE / (3R)-beta,beta-caroten-3-ol / IRON/SULFUR CLUSTER / SPHINGOSINE / Chem-SQD / Phosphatidylinositol
Similarity search - Component
Biological speciesCoelastrella (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsFadeeva, M. / Klaiman, D. / Nelson, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: To Be Published
Title: Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.
Authors: Fadeeva, M. / Klaiman, D. / Nelson, N.
History
DepositionFeb 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1 PsaA
B: Photosystem I P700 chlorophyll a apoprotein A2 PsaB
C: Photosystem I subunit VII PsaC
D: Photosystem I reaction center subunit II PsaD
E: Photosystem I reaction center subunit IV PsaE
F: Photosystem I reaction center subunit III PsaF
G: Photosystem I reaction center subunit V PsaG
I: Photosystem I reaction center subunit VIII PsaI
J: Photosystem I subunit IX PsaJ
K: Photosystem I reaction center subunit X psaK
L: Photosystem I reaction centre subunit XI PsaL
1: Light-harvesting protein of photosystem I Lhca1
Z: Light-harvesting protein of photosystem I Lhca1
3: Light-harvesting protein of photosystem I Lhca3
7: Light-harvesting protein of photosystem I Lhca7
8: Light-harvesting protein of photosystem I Lhca8
4: Light-harvesting protein of photosystem I Lhca4
5: Light-harvesting protein of photosystem I Lhca5
6: Light-harvesting protein of photosystem I Lhca6
9: Light-harvesting protein of photosystem I Lhca9
2: Light-harvesting protein of photosystem I Lhca2 partial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,389353
Polymers465,96721
Non-polymers266,421332
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 PsaA /


Mass: 82115.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 PsaB /


Mass: 81680.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)

-
Photosystem I subunit ... , 2 types, 2 molecules CJ

#3: Protein Photosystem I subunit VII PsaC /


Mass: 8780.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#9: Protein/peptide Photosystem I subunit IX PsaJ /


Mass: 4508.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)

-
Photosystem I reaction center subunit ... , 6 types, 6 molecules DEFGIK

#4: Protein Photosystem I reaction center subunit II PsaD /


Mass: 16034.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#5: Protein Photosystem I reaction center subunit IV PsaE /


Mass: 6850.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#6: Protein Photosystem I reaction center subunit III PsaF /


Mass: 17949.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#7: Protein Photosystem I reaction center subunit V PsaG /


Mass: 9806.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#8: Protein/peptide Photosystem I reaction center subunit VIII PsaI /


Mass: 4352.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#10: Protein Photosystem I reaction center subunit X psaK /


Mass: 8794.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)

-
Protein , 1 types, 1 molecules L

#11: Protein Photosystem I reaction centre subunit XI PsaL /


Mass: 12735.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)

-
Light-harvesting protein of photosystem I ... , 9 types, 10 molecules 1Z37845692

#12: Protein Light-harvesting protein of photosystem I Lhca1 /


Mass: 20671.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#13: Protein Light-harvesting protein of photosystem I Lhca3 /


Mass: 23971.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#14: Protein Light-harvesting protein of photosystem I Lhca7 /


Mass: 24091.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#15: Protein Light-harvesting protein of photosystem I Lhca8 /


Mass: 22796.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#16: Protein Light-harvesting protein of photosystem I Lhca4 /


Mass: 22609.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#17: Protein Light-harvesting protein of photosystem I Lhca5 /


Mass: 24988.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#18: Protein Light-harvesting protein of photosystem I Lhca6 /


Mass: 24911.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#19: Protein Light-harvesting protein of photosystem I Lhca9 /


Mass: 20119.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#20: Protein Light-harvesting protein of photosystem I Lhca2 partial /


Mass: 7528.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: partial / Source: (natural) Coelastrella (plant)

-
Sugars , 2 types, 8 molecules

#31: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15
#33: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

+
Non-polymers , 22 types, 392 molecules

#21: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 213 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C40H56
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#26: Chemical ChemComp-NKP / (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate / 18:1 LPA / oleoyl lysophosphatidic acid


Mass: 436.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41O7P
#27: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#28: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#29: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#30: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#32: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin / Β-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O
#34: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10
#35: Chemical ChemComp-T7X / Phosphatidylinositol / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P
#36: Chemical ChemComp-C7Z / (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O2
#37: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#38: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56O2
#39: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#40: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#41: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 704.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H77O8P
#42: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37NO2
#43: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44NO7P
#44: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Coelastrella sp. Photosystem I / Type: COMPLEX / Details: Contains 11 core subunits and 10 antenna proteins / Entity ID: #1-#19 / Source: NATURAL
Molecular weightValue: 0.9 MDa / Experimental value: YES
Source (natural)Organism: Coelastrella (plant) / Cellular location: Thylakoid membrane / Organelle: Chloroplast
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Chlorophyll concentration was provided
Specimen supportDetails: Harrick Plasma cleaner PDC-32G-2 / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K / Details: blot for 3 seconds before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 1750 nm / Nominal defocus min: 150 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.38 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 31707

-
Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2RELION3.1image acquisition
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2972135
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167160 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01352858
ELECTRON MICROSCOPYf_angle_d2.41774966
ELECTRON MICROSCOPYf_dihedral_angle_d33.24321550
ELECTRON MICROSCOPYf_chiral_restr0.1096311
ELECTRON MICROSCOPYf_plane_restr0.0139787

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more